Indeed - that's all worth trying - also, you could try using avwstats and
avwmaths to estimate the few bright voxels and threshold them out, if that
helps.
Cheers.
On Wed, 19 May 2004, Christian F. Beckmann wrote:
> Hi Russ,
>
> there are a few things you could try:
> - the command line tool 'avwroi' lets you extract an ROI, just try to
> cut off the brain stem by removing a few slices.
> - if removing a few slices does not do the trick, you could use flirt
> to register the brain to standard space, apply the inverse to e.g.
> avg152T1_brain_mask (in $FSLDIR/etc/standard ), dilate the new mask
> (avwmaths in -dils out)
> and use this to mask the original data (avwmaths in -mas mask out)
> - optimising the BET parameters: the -g option lets you specify a
> vertical gradient for driving the stimation (use negative values gives
> smaller estimates at the brainstem. Also, if the brain is not well
> located at the centre of the FOV, you can use the -c option to specify
> the initial sphere.
>
> hope this helps
> cheers
> christian
>
>
>
> On 19 May 2004, at 00:26, Russ Poldrack wrote:
>
> > hi - we're having some trouble getting BET to work properly with
> > MP-RAGE data from a Siemens Allegra. The problem is that the carotids
> > are very bright, and BET consistently includes a chunk of neck tissue
> > within the segmented brain, leading to bad registration errors with the
> > standard for some subjects. We have tried a wide range of BET
> > parameters but have not been able to prevent this. We've solved the
> > problem so far by trying to optimize BET for the rest of the brain and
> > then removing the offending sections by hand, but clearly it would be
> > nice if BET could deal with these images more adequately. Do you have
> > any suggestions about tricks that we might try (other than getting a
> > new anatomical sequence)?
> >
> > cheers,
> > russ
> >
> > ---
> > Russell A. Poldrack, Ph.D.
> > Assistant Professor of Psychology, UCLA
> > Franz Hall, Box 951563
> > Los Angeles, CA 90095-1563
> > email: [log in to unmask]
> > phone: 310.794.1224
> > fax: 310.206.5895
> > web: http://www.poldracklab.org/
> >
> --
> Christian F. Beckmann
> Oxford University Centre for Functional
> Magnetic Resonance Imaging of the Brain,
> John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> Email: [log in to unmask] - http://www.fmrib.ox.ac.uk/~beckmann/
> Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
>
Stephen M. Smith DPhil
Associate Director, FMRIB and Analysis Research Coordinator
Oxford University Centre for Functional MRI of the Brain
John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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